[Chimera-users] ViewDock descriptors problem

[Elaine Meng]

Hi Andrew,
It depends on the version of DOCK you are using - make sure you  
specify the correct version when opening the file of docked ligands.  
We have version-specific code that should show the scores for output  
from versions 3, 3.5, 3.5.x, 4, 5, 6. For example, output from  
versions 4,5,6 include comments before each ligand residue in a  
specific format interpreted by the ViewDock tool as ligand descriptors.

If PDB format, the comments look something like

REMARK     Number      : 1
REMARK     Source num  : 1
REMARK     Name        : MFCD00047559
REMARK     Description : CBZ-L-GLU_ANHYDRIDE
REMARK     Energy score                             :     -16.72
REMARK       van der Waals component                      -16.72
REMARK       electrostatic component                        0.00
REMARK     RMSD from input orientation (A)          :       1.26

If Mol2 format, the comments look something like

########## Number      : 1
########## Source num  : 22
########## Name        : test_22
########## Description : ribose-monophosphate
########## Reflect     : 0
########## Energy score                             :     -42.64
##########   intermolecular van der Waals                 -21.10
##########   intermolecular electrostatic                 -21.54
########## RMSD from input orientation (A)          :      40.86

In these examples, options under "Column...Show" would be Number,  
Source num, Name, Description, etc.

After making sure you have chosen the correct format when opening the  
file of docked ligands,
(1) look in that file with a text editor to make sure it includes the  
descriptors/values you are expecting to see in the ViewDock interface
(2) if it does contain those descriptors/values, you could send us an  
example file (e-mail to me would only be shared with a few others on  
the Chimera team)

Another option (especially if you are using some modified version of  
DOCK) is to reformat the output ligand file so that the descriptors  
appear in the form above and open it with ViewDock as "dock 4,5,6"  
output.  The basic format is

REMARK (if PDB) or ########## (if Mol2) followed by descriptor  
name, :, descriptor value

preceding each docked ligand molecule.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Jan 31, 2007, at 12:01 AM, Воронков андрей wrote:

> Dear Chimera users,
> I have ranked database from DOCK. I need to see energies of these  
> structures and their ranking. I open them by View Dock, but in the  
> field Column menu I can see only name field. Why I don't have  
> energy field there and how can I get it?
> Respectively yours,
> Andrew
>
> PS
> "Descriptors can be shown in or removed from the upper panel using  
> the Column menu." -this is from manual, but I can;t make shown any  
> descriptos but the name of the structure
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users